rs1044165

Variant names:

• chrX-66021884-G-A
• rs1044165
• NM_007268.3:c.*379C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007268.3(VSIG4):​c.*379C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 344,982 control chromosomes in the GnomAD database, including 1,844 homozygotes. There are 10,309 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.090 (491 hom., 2846 hem., cov: 23)
  • Exomes 𝑓: 0.11 (1353 hom. 7463 hem.)
• Consequence: VSIG4 NM_007268.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 16 publications found

Genes affected

VSIG4 (HGNC:17032): (V-set and immunoglobulin domain containing 4) This gene encodes a v-set and immunoglobulin-domain containing protein that is structurally related to the B7 family of immune regulatory proteins. The encoded protein may be a negative regulator of T-cell responses. This protein is also a receptor for the complement component 3 fragments C3b and iC3b. Alternate splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007268.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VSIG4	NM_007268.3	MANE Select	c.*379C>T		3_prime_UTR	Exon 8 of 8	NP_009199.1	Q9Y279-1
	VSIG4	NM_001257403.2		c.*201C>T		3_prime_UTR	Exon 8 of 8	NP_001244332.1
	VSIG4	NM_001184830.2		c.*953C>T		3_prime_UTR	Exon 7 of 7	NP_001171759.1	Q9Y279-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VSIG4	ENST00000374737.9	TSL:1 MANE Select	c.*379C>T		3_prime_UTR	Exon 8 of 8	ENSP00000363869.4	Q9Y279-1
	VSIG4	ENST00000455586.6	TSL:1	c.*953C>T		3_prime_UTR	Exon 7 of 7	ENSP00000411581.2	Q9Y279-2
	VSIG4	ENST00000968798.1		c.*379C>T		3_prime_UTR	Exon 8 of 8	ENSP00000638857.1

Frequencies

GnomAD3 genomes AF: 0.0898 AC: 10024 AN: 111661 Hom.: 492 Cov.: 23

Gnomad AFR AF: 0.0196

Gnomad AMI AF: 0.0748

Gnomad AMR AF: 0.0581

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.00169

Gnomad SAS AF: 0.0362

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.119

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.0938

GnomAD4 exome AF: 0.114 AC: 26497 AN: 233269 Hom.: 1353 Cov.: 4 AF XY: 0.105 AC XY: 7463 AN XY: 71243

African (AFR) AF: 0.0147 AC: 101 AN: 6853

American (AMR) AF: 0.0481 AC: 534 AN: 11091

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 705 AN: 5798

East Asian (EAS) AF: 0.000273 AC: 3 AN: 10984

South Asian (SAS) AF: 0.0393 AC: 1041 AN: 26460

European-Finnish (FIN) AF: 0.141 AC: 2684 AN: 19085

Middle Eastern (MID) AF: 0.137 AC: 117 AN: 852

European-Non Finnish (NFE) AF: 0.143 AC: 19978 AN: 139817

Other (OTH) AF: 0.108 AC: 1334 AN: 12329

GnomAD4 genome AF: 0.0898 AC: 10029 AN: 111713 Hom.: 491 Cov.: 23 AF XY: 0.0839 AC XY: 2846 AN XY: 33917

African (AFR) AF: 0.0196 AC: 605 AN: 30859

American (AMR) AF: 0.0581 AC: 614 AN: 10577

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 302 AN: 2642

East Asian (EAS) AF: 0.00170 AC: 6 AN: 3536

South Asian (SAS) AF: 0.0378 AC: 102 AN: 2701

European-Finnish (FIN) AF: 0.126 AC: 756 AN: 6021

Middle Eastern (MID) AF: 0.131 AC: 28 AN: 214

European-Non Finnish (NFE) AF: 0.140 AC: 7424 AN: 52958

Other (OTH) AF: 0.0926 AC: 141 AN: 1523

Alfa AF: 0.120 Hom.: 8569

Bravo AF: 0.0806

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.2
DANN	Benign	0.74
PhyloP100		0.072
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1044165; hg19: chrX-65241726;